Beast2¶

Support tier: 3

Read information about support tiers.

Installed versions¶

Resource	Version
Dardel	2.1.2, 2.3.1, 2.4.0, 2.4.8, 2.6.2, 2.6.3, 2.7.3, 2.7.4, 2.7.7

Read information about how to load this software in your environment by searching for Lmod module.

General information¶

BEAST2¶

BEAST2 is a tool for Bayesian phylogenetic analysis.

Is BEAST2 a new version of BEAST?

No.

Although BEAST and BEAST2 achieve a similar goal, BEAST and BEAST2 are developed independently.

Hence:

there are things BEAST can do that BEAST2 cannot, and vice versa
one cannot create a BEAST XML file and expect BEAST2 to be able to run it, and vice versa

Using BEAST2¶

Here is how to use BEAST2 on the PDC clusters.

1. Load a `beast2` module¶

First step is to load a BEAST2 module.

Here is how to find the BEAST2 versions on the PDC clusters:

module spider beast2

How does the result look like?

You will see something similar to this:

----------------------------------------------------------------------------------------
  beast2:
----------------------------------------------------------------------------------------
     Versions:
        beast2/2.1.2
        beast2/2.3.1
        beast2/2.4.0
        beast2/2.4.8
        beast2/2.6.2
        beast2/2.6.3
        beast2/2.7.3
        beast2/2.7.4
        beast2/2.7.7

----------------------------------------------------------------------------------------
  For detailed information about a specific "beast2" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider beast2/2.7.7
----------------------------------------------------------------------------------------

Here is how to lead a BEAST2 module:

module load beast2/2.7.7

How does the result look like?

You will see something similar to this:

beast2/2.7.7: It is recommended (but optional) to load the library BEAGLE to use with Beast2!
Please run `module spider beagle-lib` on how to load it and which versions of it that are available!

If you want to use BEAGLE too, run module spider beagle-lib and pick the CPU or GPU module.

2. Run `BEAUti`¶

BEAUti

Next step is to create a BEAST2 configuration file using BEAUti. This graphical tool can be started using:

beauti

BEAUti is a graphical program that can be launched from a remote desktop environment or when using SSH with X forwarding enabled.

After using BEAUti, save the file with your BEAST2 model.

3. Run¶

A BEAST2 run takes a lot of computing power, hence do not run it on a login node. Instead, run it in an interactive session or use a script.

How to start an interactive session?

View the PDC 'Run interactively' page.

On an interactive node, run BEAST2 on the saved BEAST2 model:

beast beast2_setup.xml

When using a script, put that line in a script. Below is an example script, called run_beast2.sh:

run_beast2.sh

#!/bin/bash
#SBATCH -A uppmax2023-2-25
module load beast2/2.7.7
beast beast2_setup.xml

In line 2, replace uppmax2023-2-25 with your PDC project
In line 3, you may want to replace beast2/2.7.7 with your favorite BEAST2 version

Then run this script using sbatch run_beast2.sh.

Note that this is a minimal script. See the PDC documentation about job scripts for ways to improve this script.

View the trees using DensiTree¶

Densitree

DensiTree is a tool that allows one to display the posterior tree distribution of a BEAST2 run.

Run:

densitree [trees_filename]

where [trees_filename] is the name of the file containing the posterior trees, resulting in, for example, densitree my_file.trees.

DensiTree is a graphical program that can be launched from a remote desktop environment or when using SSH with X forwarding enabled. As it is a CPU heavy program, run it in an interactive session.